**7. Conclusions**

Genomic studies are essential for the understanding of the *T. cruzi* pathogenicity and biology. The new sequencing technologies have contributed to improve the quality of several genomes of different strains and to elucidate the broad genetic diversity and complexity of this parasite. In this regard, the combination of long- and short-read sequencing methods may overcome the problems in the genome assembly and annotation due to the high intrinsic genome complexity of *T. cruzi*. Therefore, we need to wonder if the CL Brener genome is the best as reference in the databases, considering the new genomes of other strains that were obtained with these sequencing methods that have improved both assembly and annotation processes.

The study of the different repetitive sequences, recombination processes, and gene expansion events of the *T. cruzi* genome shows that genome plasticity plays a key role as a survival strategy during the life cycle of the parasite. Therefore, further research is needed to understand these relevant processes of the parasite biology.

Regarding the principal multi-gene families of *T. cruzi*, this parasite presents a wide variety of surface proteins with important roles in its life cycle. Due to the fact of genome plasticity, these multi-gene families have suffered an expansion and constant evolution that have increased the *T. cruzi* ability of adaptation, survival, and infection of both insect and mammalian hosts.

Altogether, the recent advances in trans-sialidases, mucins, and other multi-gene families can positively increase the current knowledge of host-parasite interactions and will allow the design of effective drugs against the Chagas disease. However, due to the genome complexity of the parasite more studies to unravel the specific structure and functions of those proteins will be needed. In this regard, high-throughput technologies will be useful to establish the development and evolution of multi-gene families of *T. cruzi*.

**Author Contributions:** M.F. conceived the idea; N.G. and M.F. acquired funding; A.H.-C. wrote the manuscript; M.F., N.G. and F.C.-H. reviewed and edited the manuscript. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by: "Ministerio de Economía y competitividad" and "Fondo Europeo de Desarrollo Regional" (SAF2016-75988-R (MINECO/FEDER) to M.F.); "Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación" and "Fondo Europeo de Desarrollo Regional" (PGC2018-096132-B-I00 (MICINN/FEDER) to N.G.); "Red de Investigación de Centros de Enfermedades Tropicales" (RICET RD16/0027/0006 to M.F.); and Comunidad de Madrid (S2017/BMD-3671 to M.F.).

**Acknowledgments:** CBMSO institutional grants from "Fundación Ramón Areces" and "Banco de Santander".

**Conflicts of Interest:** The authors declare no conflict of interest.
